This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We calculate a potential of mean force as a distance of two centers of masses of two domains in a protein PDC-109. We use a thermodynamic integration with 3000 water molecules in a periodic boundary condition. To compare between explicit and implicit model results, we also implement two implicit model calculations using a generelized Born and Poisson-Boltzmann methods. Considering the effect of different orientations of one domain, we conduct PMF calculations in different cases.